I am sorry that you and your father have to go through that. I personally do not know how you are feeling, and currently cannot imagine how you are feeling. I do know that this is something that a lot of people have a hard time with, and your comment implied that it is hard for you. I do know how it feels to lose loved ones, including my father when I was 12 years old, but that was long ago and the pain has been dulled and evaporated. I wish for your and your father's comfort and wellbeing.
As for how God fits in this situation, if indeed they do, it is completely reasonable and natural to be angry with God (if you believe in them at all or entertain the idea that they may exist), it is however not an argument against the existence of God, or an argument against religion (some religions don't even have deities), or an argument against the compatibility of science and religion. It may conceivably be an argument against God having one or all of the following characteristics, omnipotence (all-powerful), omniscience (all-knowing), benevolence (all-loving, all-good), etc... It is the problem of suffering/evil, however religions that come across this problem have theologians that offer a responses, called theodicies, to the problem of suffering/evil.
I am sorry, if I came across as callous. It is not and was not my intention.